[gmx-users] Re: 3 covalent bonds protein- heme

Thomas Schlesier schlesi at uni-mainz.de
Thu Sep 17 16:04:01 CEST 2009

Yes, you must put the heme and the protein in the same topology file (or
.itp file). The problem is you can only make bonds (angles, etc) between
atoms which are in the same [ moleculetype ] section.
Best is to write a simple script which merges the two topologies
together. You must only be aware that the atom-, chargegroup- and
residues numbers are right.
If you begin with the protein and the last atom is 'n', then the first
atom of the heme must be 'n+1' (same for chargegroups, etc).


> Dear Friends,
> I have to make three covalent bonds between the protein and the heme group.
> I have parameters for heme and the residues.
> Do I have to make as if everything belongs to the same molecule?  (as  
> it realy is)
> Has anyone done something like this?
> Thanks
> Alberto

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